On the basis of metapopulation, this paper introduce the predators preference for prey into apparent competition model and a new apparent competition system is constructed. By dynamical analysis and considerable computer simulation of the system, we investigate the effects of predator′s preference for prey on the dynamics of the coexistence equilibria. The results show: (1) the suitable changing predators preference for prey will improve the coexistence of species; (2) patch destruction is closely related to predators preference for prey; (3) the suitable increasing predators preference for the superior prey will lead to the shorter steady time; (4) The abundance of the prey have a negative correlation with the predators preference for this prey and the fragmentation of the region occupied by the prey have a positive correlation with the predators preference for this prey; (5) the polyphagous predator is more easier to survival than the monophagous predator in a destroyed patch. The results provide a theoretical basis for biodiversity conservation and sustainable development.